Abstract
Many organisms possess repetitive DNA in their genomes. These repeats are located in extragenic regions.
Some of them perform regulatory functions. One group of bacterial repeats are Repetitive Extragenic Palindromes (REPs).
By extensive in silico analysis of bacterial genomic sequences we noticed a connection between REP elements and a group of tyrosine transposases of the IS200/ IS605 family (REP-Associated tYrosine Transposases, RAYTs). The genes coding for all identified RAYTs are flanked by two REPs in inverted orientation.
REP palindromicity and inverted repeat arrangement are evolutionarily preserved. All REP sequences contain a 5´-GT(A/G)G-3´ tetranucleotide and an imperfect palindrome downstream of it.
REPs are strain-specific and their high abundance is conditioned by the presence of their cognate RAYT. RAYTs are regularly present in genomes of enteric bacteria, Pseudomonas, Xanthomonas and Stenotrophomonas gammaproteobacteria and Verrucomicrobia, where they flank REPs.